This invention relates to reaction vessels for carrying out steps in the synthesis of a chemical compound. More particularly, the invention relates to devices for the manufacture of supports having bound to the surfaces thereof a plurality of chemical compounds, such as biopolymers, which are prepared on the surface in a series of steps.
In the field of diagnostics and therapeutics, it is often useful to attach species to a surface. One important application is in solid phase chemical synthesis wherein initial derivatization of a substrate surface enables synthesis of polymers such as oligonucleotides and peptides on the substrate itself. Support bound oligomer arrays, particularly oligonucleotide arrays, may be used in screening studies for determination of binding affinity. Modification of surfaces for use in chemical synthesis has been described. See, for example, U.S. Pat. No. 5,624,711 (Sundberg), U.S. Pat. No. 5,266,222 (Willis) and U.S. Pat. No. 5,137,765 (Farnsworth).
Determining the nucleotide sequences and expression levels of nucleic acids (DNA and RNA) is critical to understanding the function and control of genes and their relationship, for example, to disease discovery and disease management. Analysis of genetic information plays a crucial role in biological experimentation. This has become especially true with regard to studies directed at understanding the fundamental genetic and environmental factors associated with disease and the effects of potential therapeutic agents on the cell. Such a determination permits the early detection of infectious organisms such as bacteria, viruses, etc.; genetic diseases such as sickle cell anemia; and various cancers. This paradigm shift has lead to an increasing need within the life science industries for more sensitive, more accurate and higher-throughput technologies for performing analysis on genetic material obtained from a variety of biological sources.
Unique or misexpressed nucleotide sequences in a polynucleotide can be detected by hybridization with a nucleotide multimer, or oligonucleotide, probe. Hybridization is based on complementary base pairing. When complementary single stranded nucleic acids are incubated together, the complementary base sequences pair to form double stranded hybrid molecules. These techniques rely upon the inherent ability of nucleic acids to form duplexes via hydrogen bonding according to Watson-Crick base-pairing rules. The ability of single stranded deoxyribonucleic acid (ssDNA) or ribonucleic acid (RNA) to form a hydrogen bonded structure with a complementary nucleic acid sequence has been employed as an analytical tool in molecular biology research. An oligonucleotide probe employed in the detection is selected with a nucleotide sequence complementary, usually exactly complementary, to the nucleotide sequence in the target nucleic acid. Following hybridization of the probe with the target nucleic acid, any oligonucleotide probe/nucleic acid hybrids that have formed are typically separated from unhybridized probe. The amount of oligonucleotide probe in either of the two separated media is then tested to provide a qualitative or quantitative measurement of the amount of target nucleic acid originally present.
Direct detection of labeled target nucleic acid hybridized to surface-bound polynucleotide probes is particularly advantageous if the surface contains a mosaic of different probes that are individually localized to discrete, known areas of the surface. Such ordered arrays containing a large number of oligonucleotide probes have been developed as tools for high throughput analyses of genotype and gene expression. Oligonucleotides synthesized on a solid support recognize uniquely complementary nucleic acids by hybridization, and arrays can be designed to define specific target sequences, analyze gene expression patterns or identify specific allelic variations. The arrays may be used for conducting cell study, for diagnosing disease, identifying gene expression, monitoring drug response, determination of viral load, identifying genetic polymorphisms, analyze gene expression patterns or identify specific allelic variations, and the like.
In one approach, cell matter is lysed, to release its DNA as fragments, which are then separated out by electrophoresis or other means, and then tagged with a fluorescent or other label. The resulting DNA mix is exposed to an array of oligonucleotide probes, whereupon selective binding to matching probe sites takes place. The array is then washed and interrogated to determine the extent of hybridization reactions. In one approach the array is imaged so as to reveal for analysis and interpretation the sites where binding has occurred. Arrays of different chemical probe species provide methods of highly parallel detection, and hence improved speed and efficiency, in assays. Assuming that the different sequence polynucleotides were correctly deposited in accordance with the predetermined configuration, then the observed binding pattern will be indicative of the presence and/or concentration of one or more polynucleotide components of the sample.
The arrays may be microarrays created by in-situ synthesis, oligonucleotide deposition or cDNA. In general, arrays are synthesized on a surface of a substrate by one of any number of synthetic techniques that are known in the art. In one approach to the synthesis of microarrays flow cells or flow devices are employed in which a substrate is placed to carry out the synthesis.
One embodiment of the present invention is a flow device, which includes a housing comprising a housing chamber. The housing has an opening adapted for insertion of a support into the housing chamber. A sealing member is movably mounted in the housing chamber and adapted to engage the support to form a reagent chamber between a surface of the support and a surface of the sealing member. A mechanism is included for moving the sealing member within the housing chamber. The device has both an inlet and an outlet, which are both in fluid communication with the reagent chamber. In one embodiment a wall of the device comprises a viewing area such as, for example, a window, for viewing the surface of a support that is inserted into the housing chamber.
Another embodiment of the present invention is a flow device comprising a housing with a housing chamber. An opening is provided in the housing and is adapted for insertion of a holding element comprising a support into the housing chamber. A sealing member is movably mounted in the housing chamber and adapted to engage the support to form a reagent chamber between a surface of the support and a surface of the sealing member. The sealing member is attached to a pressure-activated mechanism for moving the sealing member within the housing chamber. The device also comprises a mechanism adapted to engage the support on a surface opposite the surface engaged by the sealing member. The device has an inlet and an outlet, both of which are in fluid communication with the reagent chamber. One wall of the housing has a viewing area adapted for viewing a surface of the support.
Another embodiment of the present invention is a method for performing a step of a chemical reaction on the surface of a support. A support is placed into a chamber of a device such as described above. The mechanism adapted to engage the support on a surface opposite the surface engaged by the sealing member is activated to urge the support toward the sealing member. The pressure-activated mechanism is activated to urge the support against the aforesaid mechanism and against an interior wall of the housing chamber to form the reagent chamber. A fluid reagent for conducting the reaction step is introduced into the reagent chamber by means of the inlet. Thereafter, the fluid reagent is removed from the reagent chamber. The pressure-activated mechanism is deactivated and the support is removed from the housing chamber.
Another embodiment of the present invention is a method for performing a step of a chemical reaction on the surface of a support. A support is placed into a chamber of a device. A mechanism is activated to engage the support on a surface thereof. A pressure-activated mechanism is activated for moving a sealing member within the chamber to engage a surface of the support opposite the surface engaged by the above mechanism, which is then deactivated thereby forming a reagent chamber. A fluid reagent for conducting the reaction step is introduced into the reagent chamber. After a period of time, the fluid reagent is removed from the reagent chamber. The pressure-activated mechanism is deactivated and the support is removed from the chamber.
Another embodiment of the present invention is a method for synthesizing a plurality of biopolymers on the surface of a support. The synthesis comprises a plurality of monomer additions. After each of the monomer additions, the support is placed into a chamber of a first device as described above. The surface of the support is subjected to a first step of the synthesis that is subsequent to a monomer addition. Then, the support is placed into a chamber of a second device as described above. The surface of the support is subjected to a second step of the synthesis that is subsequent to the first step.
Another embodiment of the present invention is an apparatus for synthesizing an array of biopolymers on the surface of a support. The apparatus comprises a platform on which are mounted a plurality of devices as described above. The apparatus also comprises one or more fluid dispensing stations mounted on the platform. The stations are in fluid communication with one or more of the devices. A station for monomer addition to the surface of the support is mounted on the platform. The apparatus also comprises a mechanism, which comprises a holding element for moving a support to and from the station for monomer addition and one of the devices and from one of the devices to another of the devices. The apparatus optionally comprises a mechanism for rotating the devices.
Another embodiment of the present invention is a device for transferring a support from one flow cell to another flow cell. The device comprises a vacuum actuated element for holding the support and a mechanism for moving the vacuum actuated element from one flow cell to another flow. The mechanism may be part of a robotic arm and the vacuum actuated element may comprise at least two prongs.